This is an R Markdown Notebook. When you execute code within the notebook, the results appear beneath the code.
Load the required libraries. If you don’t have them installed, please do by running install.packages()
library(plotly)## Loading required package: ggplot2##
## Attaching package: 'plotly'## The following object is masked from 'package:ggplot2':
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## last_plot## The following object is masked from 'package:stats':
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## filter## The following object is masked from 'package:graphics':
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## layoutlibrary(stringr)
library(reshape2)
library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
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## filter, lag## The following objects are masked from 'package:base':
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## intersect, setdiff, setequal, unionlibrary(readr)Load the NMR binned csv. Just adapt the path to location of your file. You can use autocompletion using the tab key
Binning_Fusarium_sh1 <- read_csv("../../data/Binning_Fusarium_matz_center.csv")## Warning: Duplicated column names deduplicated: '-115.03' => '-115.03_1' [146],
## '702.028' => '702.028_1' [283], '1675.59' => '1675.59_1' [286],
## '-314.082' => '-314.082_1' [308], '-402.228' => '-402.228_1' [326],
## '-202.469' => '-202.469_1' [331], '-240.71' => '-240.71_1' [495],
## '313.821' => '313.821_1' [599], '443.177' => '443.177_1' [614],
## '-168.964' => '-168.964_1' [628], '-161.33' => '-161.33_1' [637],
## '-305.105' => '-305.105_1' [661], '65.8555' => '65.8555_1' [730],
## '281.871' => '281.871_1' [735], '785.014' => '785.014_1' [778], '221.152'
## => '221.152_1' [803], '141.064' => '141.064_1' [830], '-195.684' =>
## '-195.684_1' [865], '146.084' => '146.084_1' [874], '-49.4336' =>
## '-49.4336_1' [877], '96.0381' => '96.0381_1' [903], '-4.61914' =>
## '-4.61914_1' [921], '-40.5273' => '-40.5273_1' [923], '-57.3506' =>
## '-57.3506_1' [963], '-77.3545' => '-77.3545_1' [965], '-135.034' =>
## '-135.034_1' [982], '-121.533' => '-121.533_1' [986], '-135.883' =>
## '-135.883_1' [1002], '-168.964' => '-168.964_2' [1039], '-21.3008'
## => '-21.3008_1' [1041], '11.0029' => '11.0029_1' [1055], '134.562'
## => '134.562_1' [1058], '-200.207' => '-200.207_1' [1066], '52.9902'
## => '52.9902_1' [1077], '58.3623' => '58.3623_1' [1099], '-0.519531'
## => '-0.519531_1' [1131], '-130.652' => '-130.652_1' [1138], '158.453'
## => '158.453_1' [1140], '166.3' => '166.3_1' [1153], '92.4326' =>
## '92.4326_1' [1156], '-10.7686' => '-10.7686_1' [1160], '-36.7812'
## => '-36.7812_1' [1166], '131.098' => '131.098_1' [1174], '-150.373'
## => '-150.373_1' [1179], '149.265' => '149.265_1' [1190], '47.6885'
## => '47.6885_1' [1216], '10.7197' => '10.7197_1' [1225], '-60.6729'
## => '-60.6729_1' [1232], '-268.419' => '-268.419_1' [1236], '24.998'
## => '24.998_1' [1253], '-96.9346' => '-96.9346_1' [1264], '207.086'
## => '207.086_1' [1265], '-87.4629' => '-87.4629_1' [1276], '105.51'
## => '105.51_1' [1285], '50.2334' => '50.2334_1' [1288], '56.2412' =>
## '56.2412_1' [1293], '-26.1777' => '-26.1777_1' [1314], '-229.471'
## => '-229.471_1' [1318], '70.3086' => '70.3086_1' [1333], '-63.8535'
## => '-63.8535_1' [1342], '28.8857' => '28.8857_1' [1343], '86.5664'
## => '86.5664_1' [1345], '8.95312' => '8.95312_1' [1353], '43.8008'
## => '43.8008_1' [1354], '-5.4668' => '-5.4668_1' [1355], '-4.61914'
## => '-4.61914_2' [1361], '62.6035' => '62.6035_1' [1388], '75.8213'
## => '75.8213_1' [1395], '-67.2471' => '-67.2471_1' [1400], '22.666'
## => '22.666_1' [1410], '104.309' => '104.309_1' [1414], '19.9795' =>
## '19.9795_1' [1425], '26.3418' => '26.3418_1' [1428], '-10.415' =>
## '-10.415_1' [1431], '-75.5879' => '-75.5879_1' [1440], '-55.584' =>
## '-55.584_1' [1441], '4.64062' => '4.64062_1' [1444], '52.9902' =>
## '52.9902_2' [1456], '-85.625' => '-85.625_1' [1457], '-266.369' =>
## '-266.369_1' [1459], '-126.199' => '-126.199_1' [1472], '65.502' =>
## '65.502_1' [1506], '-126.128' => '-126.128_1' [1508], '-74.7393' =>
## '-74.7393_1' [1523], '-8.29492' => '-8.29492_1' [1540], '-82.0908'
## => '-82.0908_1' [1544], '-103.721' => '-103.721_1' [1554], '-19.958'
## => '-19.958_1' [1558], '18.3545' => '18.3545_1' [1572], '-116.373' =>
## '-116.373_1' [1578], '827.072' => '827.072_1' [1602]##
## ── Column specification ────────────────────────────────────────────────────────
## cols(
## .default = col_double()
## )
## ℹ Use `spec()` for the full column specifications.Lets have a look at the first rows of this file
head(Binning_Fusarium_sh1)OK. Be sure to have ppm on the columns and fraction numbers as rows. Now we transform the dataframe as a matrix
DTz <- as.matrix(data.frame(Binning_Fusarium_sh1))Lets have a look at the structure of the file
str(DTz)## num [1:134, 1:1602] -12215 -13266 -12792 -12116 -12881 ...
## - attr(*, "dimnames")=List of 2
## ..$ : NULL
## ..$ : chr [1:1602] "X.14393.5" "X358.495" "X.14208.8" "X602.433" ...Now we’ll remove the row indexes
DTz <- DTz[,-1] And we set the matrix row and colnames according to the ones of the df
colnames(DTz) <- colnames(Binning_Fusarium_sh1)[-1]
rownames(DTz) <- rownames(Binning_Fusarium_sh1)Let’s transform these data in the long form
mtrx.melt <- melt(DTz, id.vars = c('sample', 'ppm'), measure.vars = 'int')
names(mtrx.melt) <- c('sample', 'ppm', 'int')Now we can plot a quick 3Dplot to have an overview of the data
p <- plot_ly(z = ~DTz) %>% add_surface()
pOK so now we want to remove the annoying signals corresponding to the solvents. We can check at the colunms name and note their numbers. Example its DMSO > signals at 2.5 ppm I want to delete columns 350,351 and 352.
colnames(DTz)## [1] "358.495" "-14208.8" "602.433" "-953.72" "-696.635"
## [6] "-713.104" "-655.849" "-586.647" "-556.252" "-456.443"
## [11] "-367.592" "-187.201" "-35.2256" "14.4658" "-106.619"
## [16] "358.354" "129.261" "339.622" "187.93" "383.023"
## [21] "424.374" "402.179" "342.52" "118.799" "165.169"
## [26] "534.361" "473.147" "100.421" "379.064" "231.26"
## [31] "382.67" "390.162" "368.179" "527.223" "493.435"
## [36] "601.23" "27.0488" "401.118" "463.322" "272.895"
## [41] "454.628" "358.637" "478.591" "144.246" "303.572"
## [46] "444.52" "131.098" "138.874" "215.568" "112.366"
## [51] "222.071" "175.843" "208.217" "67.127" "175.983"
## [56] "276.287" "389.385" "260.807" "153.576" "134.562"
## [61] "65.8555" "200.229" "341.389" "118.092" "416.599"
## [66] "213.659" "-26.1777" "-19.4629" "215.427" "214.296"
## [71] "81.4766" "-25.4717" "55.8174" "-95.0967" "138.096"
## [76] "81.6182" "313.821" "35.248" "64.0176" "3.50977"
## [81] "182.274" "8.1748" "187.223" "74.1963" "26.9072"
## [86] "160.928" "139.651" "-67.5293" "85.2227" "134.42"
## [91] "129.967" "-126.199" "-7.58789" "-163.804" "235.36"
## [96] "15.8799" "50.5166" "98.3701" "83.668" "-37.6289"
## [101] "-328.148" "-126.411" "-33.1055" "-112.839" "-40.5273"
## [106] "22.3125" "-103.297" "43.8008" "-217.879" "75.1855"
## [111] "-106.76" "-161.188" "10.5781" "-190.24" "-218.444"
## [116] "-10.9102" "12.1338" "-67.1055" "-1.93262" "-115.03"
## [121] "-182.677" "-282.697" "-295.421" "-29.2178" "-137.509"
## [126] "-132.561" "-177.022" "-5.4668" "-43.3545" "-114.96"
## [131] "-135.388" "-185.434" "7.18555" "-188.968" "-176.244"
## [136] "-231.309" "-255.201" "-148.183" "-16.4941" "-171.367"
## [141] "-18.6855" "-222.402" "-103.014" "-202.469" "-115.03_1"
## [146] "-161.684" "-252.373" "-80.1826" "-398.481" "-320.231"
## [151] "-280.789" "-390.141" "-185.646" "-305.105" "-216.041"
## [156] "-293.229" "-293.583" "-201.196" "-419.97" "-213.354"
## [161] "16.5166" "-260.573" "-82.2324" "-274.074" "-260.36"
## [166] "-207.912" "-412.053" "-361.725" "-345.679" "-240.71"
## [171] "-237.671" "-270.964" "-179.284" "-402.228" "-68.3066"
## [176] "-473.055" "-346.881" "-147.546" "-222.897" "-375.014"
## [181] "-325.392" "-122.17" "-234.631" "-163.168" "16.1631"
## [186] "-125.28" "-62.1572" "37.0146" "238.611" "240.449"
## [191] "220.375" "-268.419" "-364.976" "-150.373" "-301.005"
## [196] "-95.6621" "26.3418" "-14.0205" "-138.145" "11.2852"
## [201] "207.086" "-256.332" "-63.8535" "-296.905" "224.263"
## [206] "1341.88" "548.146" "5301.35" "5063.42" "504.744"
## [211] "785.014" "1032.34" "2084.08" "1927.37" "1625.75"
## [216] "2876.54" "3343.21" "2368.95" "942.149" "435.189"
## [221] "449.114" "456.819" "425.646" "1371.99" "3039.19"
## [226] "1787.41" "3315.29" "5336.48" "2003.22" "1695.31"
## [231] "933.172" "1047.54" "536.199" "371.431" "388.678"
## [236] "87.6973" "-13.9492" "394.757" "576.915" "44.3662"
## [241] "-174.194" "141.56" "4278.17" "-44.1328" "-158.715"
## [246] "-246.365" "-195.612" "58.2207" "-113.829" "-77.3545"
## [251] "15.0322" "264.482" "160.786" "177.397" "336.724"
## [256] "116.184" "186.728" "-200.065" "-396.148" "-254.564"
## [261] "-195.4" "173.156" "-237.176" "-279.729" "-324.826"
## [266] "-101.529" "212.316" "48.5371" "-82.0908" "-22.7852"
## [271] "-255.13" "-368.581" "-30.9141" "-538.935" "-279.517"
## [276] "-169.388" "-275.629" "-353.808" "-3.7002" "42.8115"
## [281] "702.028" "702.028_1" "443.177" "1675.59" "1675.59_1"
## [286] "3295.85" "876.341" "582.146" "104.309" "82.6074"
## [291] "-288.211" "-133.196" "-173.982" "-404.065" "-125.351"
## [296] "-367.309" "-435.662" "-228.835" "-196.249" "-209.325"
## [301] "-294.714" "1009.94" "-382.931" "674.249" "-253.363"
## [306] "-314.082" "-314.082_1" "-392.826" "-453.687" "-438.772"
## [311] "-55.3711" "205.106" "-313.375" "102.965" "-49.4336"
## [316] "-21.3008" "-333.238" "-133.55" "-625.312" "-491.15"
## [321] "-492.493" "-322.776" "-440.539" "-321.504" "-402.228_1"
## [326] "-431.916" "-122.735" "-474.186" "-516.88" "-202.469_1"
## [331] "-203.741" "-32.3281" "539.31" "-479.487" "20389"
## [336] "613.671" "1259.53" "-1378.61" "-415.729" "460.07"
## [341] "1321.87" "45321.9" "43390.2" "5332.88" "10040.9"
## [346] "28657.8" "19250.2" "8769" "8787.37" "14597.5"
## [351] "29674.7" "102524" "757484" "1.90E+07" "1.18E+06"
## [356] "243020" "51894.9" "31236" "16133.4" "10413.5"
## [361] "9314.48" "12067.1" "2887.78" "4589.76" "94192.6"
## [366] "23062.5" "3709.29" "2056.02" "2069.94" "2199.86"
## [371] "466.433" "978.765" "1028.95" "1126.99" "497.888"
## [376] "511.247" "869.483" "625.829" "810.391" "960.527"
## [381] "804.382" "1169.62" "986.822" "234.865" "547.227"
## [386] "166.3" "220.233" "201.147" "244.974" "202.208"
## [391] "175.206" "122.051" "354.749" "-44.2734" "187.294"
## [396] "49.8096" "2.37891" "320.042" "1342.58" "8941.33"
## [401] "374.541" "237.41" "29.0273" "445.722" "566.807"
## [406] "453.779" "519.164" "454.274" "678.49" "496.615"
## [411] "1070.02" "583.135" "1236.49" "2219.8" "7940.13"
## [416] "4900.78" "965.192" "1429.6" "1358.49" "2152.93"
## [421] "4612.59" "1993.96" "1921.15" "2810.38" "3361.09"
## [426] "4272.38" "5766.89" "5625.09" "8655.61" "12033.3"
## [431] "20393" "33175.1" "61905.3" "152525" "1.02E+06"
## [436] "1.46E+06" "166382" "60913.6" "35899.1" "21488.9"
## [441] "14860.4" "10017.4" "8240.55" "6283.18" "6664.39"
## [446] "5805.91" "4730.49" "3903.4" "3366.47" "3749.51"
## [451] "6450.78" "9137.55" "7284.45" "4554.34" "3685.05"
## [456] "3187.7" "4872.08" "4623.83" "5808.74" "4348.36"
## [461] "3160.49" "3705.55" "3552.3" "4774.6" "4690.84"
## [466] "3299.1" "2635.29" "2124.16" "3312.32" "2817.24"
## [471] "2975.64" "2190.11" "1752.49" "1780.2" "1352.62"
## [476] "2181.84" "1490.81" "2415.25" "1979.75" "2486.85"
## [481] "1079.7" "928.224" "635.584" "645.621" "294.029"
## [486] "1018.91" "3302.57" "1729.1" "528.989" "92.4326"
## [491] "309.792" "591.971" "180.225" "-240.71_1" "147.709"
## [496] "213.589" "-230.249" "420.91" "4956.76" "2161.48"
## [501] "170.471" "15.7383" "5.91309" "1053.2" "2762.24"
## [506] "1944.41" "212.67" "-65.9746" "-134.822" "-144.012"
## [511] "281.871" "1071.93" "662.232" "285.052" "52.4951"
## [516] "971.555" "2295.57" "1846.15" "0.258789" "-119.342"
## [521] "76.2461" "649.438" "1358.14" "358.849" "58.3623"
## [526] "-59.1885" "-59.9658" "57.8672" "86.7783" "216.486"
## [531] "180.437" "-141.325" "239.46" "519.729" "746.844"
## [536] "585.68" "743.451" "870.05" "1033.69" "3647.23"
## [541] "6732.18" "4759.83" "1569.49" "1024.22" "811.31"
## [546] "827.991" "1163.33" "3082.59" "3521.62" "895.214"
## [551] "509.339" "689.8" "150.325" "96.0381" "310.711"
## [556] "232.815" "400.978" "132.653" "18.9199" "-34.8018"
## [561] "141.064" "656.295" "690.719" "1531.81" "1279.82"
## [566] "409.035" "524.466" "208.57" "946.531" "2024.78"
## [571] "3222.97" "2476.95" "258.403" "152.304" "44.6494"
## [576] "186.516" "154.354" "225.464" "143.468" "148.981"
## [581] "261.584" "-4.61914" "169.764" "341.247" "600.1"
## [586] "601.867" "221.152" "19.7676" "172.308" "-180.839"
## [591] "-49.0098" "-268.489" "-252.444" "213.377" "-160.34"
## [596] "-402.439" "-53.3926" "313.821_1" "-56.502" "-38.4072"
## [601] "-135.883" "-456.797" "-132.277" "-95.0264" "-185.01"
## [606] "116.325" "187.081" "115.83" "103.318" "2187.71"
## [611] "4368.23" "986.187" "443.177_1" "329.867" "97.2393"
## [616] "-168.964" "91.0898" "29.8047" "560.939" "1628.58"
## [621] "307.601" "-264.814" "-161.33" "-36.4277" "-116.373"
## [626] "696.232" "-168.964_1" "-129.309" "-427.745" "-324.332"
## [631] "-98.7021" "56.2412" "-150.586" "-101.741" "-227.562"
## [636] "-161.33_1" "-242.194" "-195.684" "1742.31" "1608.15"
## [641] "716.52" "1171.03" "2055.81" "1557.68" "1317.7"
## [646] "8813.17" "2267.93" "-130.652" "-333.874" "-376.215"
## [651] "-273.791" "-407.67" "-413.396" "-656.344" "-491.574"
## [656] "-314.647" "-120.049" "-245.658" "-317.546" "-305.105_1"
## [661] "-382.012" "-447.184" "-126.128" "-187.413" "8.74023"
## [666] "-158.148" "998.769" "-20.3115" "-374.165" "-456.655"
## [671] "-266.369" "-39.3965" "-307.861" "-252.091" "-302.207"
## [676] "-212.365" "-172.64" "-139.771" "415.256" "1755.18"
## [681] "565.676" "-154.261" "-55.8662" "-305.953" "-526.564"
## [686] "-29.4297" "-525.646" "-156.877" "2170.53" "2577.54"
## [691] "-167.268" "-336.984" "-199.712" "-367.662" "-478.427"
## [696] "-370.772" "-534.552" "-194.481" "-389.857" "-419.334"
## [701] "-210.244" "-200.207" "-212.224" "47.6885" "-432.41"
## [706] "-296.41" "-337.126" "-198.864" "-268.914" "-148.253"
## [711] "-381.021" "-215.829" "-283.192" "-67.0342" "38.0049"
## [716] "25.7764" "-212.082" "-110.224" "11.0029" "-355.504"
## [721] "81.123" "-232.652" "-346.668" "-149.879" "-152.282"
## [726] "173.58" "-36.71" "99.7842" "65.8555_1" "190.828"
## [731] "454.84" "162.129" "38.5703" "281.871_1" "-93.4717"
## [736] "457.313" "555.002" "708.603" "417.729" "187.718"
## [741] "305.057" "158.312" "-72.9014" "23.5137" "157.817"
## [746] "290" "441.551" "1382.1" "175.277" "224.05"
## [751] "461.838" "494.354" "152.516" "217.265" "381.326"
## [756] "682.236" "370.865" "422.042" "17.7881" "64.9365"
## [761] "283.073" "137.46" "289.576" "176.479" "164.108"
## [766] "213.801" "199.805" "492.445" "486.86" "696.374"
## [771] "511.459" "629.293" "498.807" "625.547" "582.641"
## [776] "570.623" "785.014_1" "705.775" "909.28" "747.339"
## [781] "694.678" "815.833" "542.35" "244.479" "371.854"
## [786] "193.16" "-51.2715" "59.1396" "-140.689" "938.049"
## [791] "623.497" "200.865" "6.76172" "105.51" "348.245"
## [796] "264.978" "258.475" "39.3477" "213.447" "242.217"
## [801] "396.241" "221.152_1" "430.736" "1800.98" "432.361"
## [806] "181.215" "281.518" "736.947" "473.854" "623.709"
## [811] "1961.87" "671.917" "-57.2803" "95.6143" "100.986"
## [816] "58.4326" "124.383" "65.502" "173.015" "176.267"
## [821] "398.009" "76.9531" "21.6758" "113.073" "107.701"
## [826] "64.2295" "50.2334" "258.263" "141.064_1" "433.775"
## [831] "1577.19" "1939.1" "1895.99" "2033.47" "5548.68"
## [836] "1346.05" "528.282" "326.898" "560.586" "1979.89"
## [841] "10791.3" "-50.4238" "196.129" "62.6035" "77.165"
## [846] "146.084" "-264.531" "-17.8369" "-215.122" "-24.835"
## [851] "-227.351" "-229.471" "-192.644" "-113.617" "-66.2568"
## [856] "-128.743" "-339.883" "-117.575" "-141.396" "-1.5791"
## [861] "-34.166" "18.4248" "-185.504" "-195.684_1" "86.5664"
## [866] "-154.12" "149.265" "-13.3135" "50.7285" "124.171"
## [871] "-99.4795" "-15.0098" "146.084_1" "-154.474" "-60.6729"
## [876] "-49.4336_1" "-70.8516" "-62.6523" "-172.286" "-37.417"
## [881] "-173.417" "-164.511" "-362.644" "-172.428" "-204.519"
## [886] "-135.034" "259.817" "49.5264" "1179.65" "2135.05"
## [891] "241.58" "21.3936" "301.381" "104.661" "6.5498"
## [896] "201.431" "410.661" "648.802" "388.748" "223.556"
## [901] "282.437" "96.0381_1" "276.782" "-100.61" "-181.97"
## [906] "259.676" "1392.14" "243.56" "359.626" "379.913"
## [911] "1642.08" "1792.15" "1393.27" "1327.32" "1154.14"
## [916] "390.516" "-2.56934" "53.2725" "-162.319" "-4.61914_1"
## [921] "-104.993" "-40.5273_1" "79.0029" "-179.496" "72.8525"
## [926] "-136.448" "-291.038" "-8.50684" "130.392" "135.057"
## [931] "489.335" "420.062" "828.769" "2038.56" "6233.28"
## [936] "6566.77" "1049.52" "227.302" "90.5947" "-19.958"
## [941] "7.53906" "-55.5127" "-238.66" "-195.117" "-103.721"
## [946] "22.666" "-16.5645" "182.981" "286.254" "1721.75"
## [951] "1833.85" "896.345" "327.04" "-130.723" "128.129"
## [956] "-90.6436" "-5.82031" "-161.612" "-57.3506" "-75.5879"
## [961] "-249.334" "-57.3506_1" "-308.074" "-77.3545_1" "-302.843"
## [966] "-190.452" "-260.502" "-153.342" "-63.7832" "-109.163"
## [971] "-121.533" "-381.799" "-166.914" "-390.847" "-124.785"
## [976] "-96.0869" "-111.284" "-231.238" "50.8691" "-117.929"
## [981] "-135.034_1" "-36.2861" "-93.3301" "-179.426" "-121.533_1"
## [986] "-340.165" "-302.631" "-163.945" "-70.0039" "-117.292"
## [991] "-75.6582" "-217.454" "-221.13" "-33.459" "-68.3779"
## [996] "492.304" "3623.2" "216.346" "-76.9307" "-36.7812"
## [1001] "-135.883_1" "-47.3838" "-126.835" "-140.831" "-305.317"
## [1006] "-260.785" "-49.3633" "-94.8145" "221.364" "158.453"
## [1011] "232.32" "89.8887" "-83.7168" "111.589" "9.51855"
## [1016] "32.9863" "-117.08" "-38.8311" "7.04395" "-60.1074"
## [1021] "-96.9346" "-36.2158" "-76.4355" "14.1836" "-250.253"
## [1026] "18.001" "-108.527" "-211.588" "-301.5" "38.4287"
## [1031] "-148.96" "28.8857" "-21.6543" "-346.739" "-115.667"
## [1036] "-49.8584" "-142.81" "-168.964_2" "89.4639" "-21.3008_1"
## [1041] "206.379" "-344.124" "-144.153" "-98.3486" "-229.33"
## [1046] "-192.148" "-140.901" "-185.787" "-62.5107" "-142.174"
## [1051] "-19.3926" "4.64062" "52.9902" "11.0029_1" "-168.894"
## [1056] "-239.721" "134.562_1" "-156.594" "-218.656" "-86.8271"
## [1061] "40.9736" "-83.3633" "-58.9766" "-175.538" "-200.207_1"
## [1066] "-108.386" "71.0146" "197.331" "-1.36719" "250.84"
## [1071] "104.521" "94.9072" "-39.6084" "8.95312" "19.9795"
## [1076] "52.9902_1" "-354.02" "-5.8916" "-223.745" "-57.1387"
## [1081] "-59.6123" "-245.163" "-14.9395" "-53.6748" "-14.5859"
## [1086] "26.4824" "-184.02" "125.302" "64.2998" "-182.182"
## [1091] "-83.4336" "209.63" "-166.702" "124.595" "-110.931"
## [1096] "11.71" "-169.671" "58.3623_1" "-55.1592" "165.311"
## [1101] "-53.8164" "51.3643" "-7.23438" "-181.334" "80.5576"
## [1106] "-123.654" "-184.585" "10.7197" "-153.979" "-176.456"
## [1111] "18.3545" "-28.2285" "-12.1826" "-69.0137" "109.539"
## [1116] "-115.102" "70.3086" "-8.43555" "14.749" "78.2959"
## [1121] "713.197" "-119.555" "-10.7686" "-37.5586" "-154.686"
## [1126] "-0.519531" "-115.737" "-10.415" "-140.548" "-0.519531_1"
## [1131] "8.88184" "-107.962" "-19.6045" "117.668" "-92.623"
## [1136] "104.025" "-130.652_1" "13.123" "158.453_1" "-272.377"
## [1141] "29.9463" "-117.505" "137.248" "10.1543" "294.241"
## [1146] "-214.627" "103.39" "142.974" "-20.7354" "-46.3232"
## [1151] "77.7305" "166.3_1" "111.659" "3.86328" "92.4326_1"
## [1156] "37.793" "-144.719" "45.4268" "-10.7686_1" "-95.8037"
## [1161] "9.23535" "41.8926" "18.1416" "151.95" "-36.7812_1"
## [1166] "138.661" "-57.4922" "60.624" "-9.70801" "142.055"
## [1171] "-128.603" "-16.9893" "131.098_1" "-245.517" "-38.6895"
## [1176] "46.6279" "-197.097" "-150.373_1" "74.3369" "205.389"
## [1181] "106.287" "171.46" "186.304" "141.277" "136.541"
## [1186] "139.156" "314.882" "-58.2695" "149.265_1" "387.9"
## [1191] "-67.7412" "311.418" "147.639" "115.972" "15.3848"
## [1196] "254.304" "76.5996" "471.663" "121.768" "193.09"
## [1201] "88.6162" "323.576" "34.9648" "310.146" "97.0273"
## [1206] "243.206" "75.8213" "214.225" "-27.3096" "112.578"
## [1211] "115.547" "159.231" "-63.0059" "195.281" "47.6885_1"
## [1216] "225.747" "135.834" "217.193" "170.399" "-107.043"
## [1221] "-5.11328" "-145.354" "24.998" "10.7197_1" "-79.8994"
## [1226] "92.8574" "-39.5381" "37.0859" "-188.402" "-87.4629"
## [1231] "-60.6729_1" "162.624" "100.067" "101.269" "-268.419_1"
## [1236] "274.379" "-165.006" "53.5557" "-124.361" "-110.012"
## [1241] "-129.662" "-27.7334" "-11.1924" "-85.625" "126.716"
## [1246] "-2.70996" "-33.8125" "216.699" "153.859" "54.0508"
## [1251] "110.175" "24.998_1" "-213.566" "79.7803" "-50.918"
## [1256] "87.4141" "-259.159" "-90.4316" "9.30664" "43.5186"
## [1261] "-30.1367" "-117.222" "-96.9346_1" "207.086_1" "-74.7393"
## [1266] "331.352" "-158.927" "47.5469" "69.8838" "35.9551"
## [1271] "-99.4092" "-4.97266" "108.62" "15.668" "-87.4629_1"
## [1276] "161.493" "125.231" "-73.3262" "51.1523" "-68.0244"
## [1281] "170.683" "198.462" "-148.395" "105.51_1" "-8.71875"
## [1286] "17.4355" "50.2334_1" "-5.67969" "74.4082" "-26.6729"
## [1291] "82.3252" "56.2412_1" "144.6" "-48.9395" "-83.5049"
## [1296] "-123.159" "59.3516" "-29.7832" "-8.29492" "37.8633"
## [1301] "229.988" "-152.353" "-11.334" "-132.702" "-147.616"
## [1306] "-62.0156" "-165.218" "-189.887" "-63.7129" "-8.01172"
## [1311] "-29.9248" "-124.502" "-26.1777_1" "-8.36523" "152.587"
## [1316] "-49.6455" "-229.471_1" "-23.9873" "102.188" "151.103"
## [1321] "60.6953" "94.4121" "-29.5" "-15.2217" "-90.5732"
## [1326] "317.214" "-16.0703" "-127.896" "29.4521" "36.8027"
## [1331] "-87.6748" "70.3086_1" "-58.4111" "-255.767" "-27.9453"
## [1336] "179.871" "-172.003" "-20.5938" "85.9297" "-16.1406"
## [1341] "-63.8535_1" "28.8857_1" "127.352" "86.5664_1" "-27.0264"
## [1346] "136.823" "-94.1074" "163.261" "-5.39648" "202.773"
## [1351] "-57.209" "8.95312_1" "43.8008_1" "-5.4668_1" "4.28711"
## [1356] "127.069" "-57.8457" "-228.27" "84.7285" "-4.61914_2"
## [1361] "-161.118" "92.0088" "-53.0391" "-9.35449" "-111.496"
## [1366] "-55.584" "246.74" "146.79" "-143.234" "204.117"
## [1371] "-150.091" "-0.166016" "247.73" "-93.8242" "72.1465"
## [1376] "277.913" "44.5078" "-38.4775" "-81.9492" "67.4102"
## [1381] "70.0254" "-180.769" "91.8672" "2.80273" "38.2168"
## [1386] "-15.1514" "62.6035_1" "18.6367" "39.7715" "-99.1963"
## [1391] "-104.781" "-30.2783" "-90.0781" "75.8213_1" "-173.771"
## [1396] "-67.2471" "52.2832" "-43.6377" "-67.2471_1" "136.895"
## [1401] "3.79297" "198.392" "41.6094" "-78.3447" "-44.7686"
## [1406] "-128.673" "86.1416" "222.919" "22.666_1" "176.055"
## [1411] "-231.592" "-169.6" "104.309_1" "-190.028" "-0.873047"
## [1416] "-45.8994" "-96.793" "12.8408" "108.974" "-25.9658"
## [1421] "28.25" "278.62" "98.583" "19.9795_1" "29.5928"
## [1426] "-43.7793" "26.3418_1" "-47.8076" "75.6094" "-10.415_1"
## [1431] "72.2168" "178.528" "80.3457" "-56.29" "-80.041"
## [1436] "76.1748" "33.3398" "-50.5645" "-75.5879_1" "-55.584_1"
## [1441] "-10.9805" "-90.29" "4.64062_1" "-95.168" "145.519"
## [1446] "71.7217" "-38.0537" "-28.5107" "276.499" "51.0107"
## [1451] "28.8154" "-207.629" "-26.3906" "76.458" "52.9902_2"
## [1456] "-85.625_1" "-82.0205" "-266.369_1" "-4.68945" "-97.0059"
## [1461] "385.851" "-33.8828" "-72.4072" "22.3828" "168.067"
## [1466] "98.8652" "8.03418" "-16.7061" "-107.82" "90.9482"
## [1471] "-126.199_1" "-80.8184" "18.2129" "89.3936" "64.6533"
## [1476] "194.856" "-196.178" "204.965" "-16.918" "-67.6006"
## [1481] "203.339" "0.612305" "-68.5195" "-31.4092" "30.4414"
## [1486] "-104.852" "-116.727" "-3.34668" "222.212" "5.98438"
## [1491] "132.017" "-197.733" "-87.0391" "135.339" "-101.671"
## [1496] "19.626" "-100.257" "-73.9619" "71.8633" "59.5635"
## [1501] "-38.3359" "20.1211" "-42.7891" "-50.7773" "65.502_1"
## [1506] "-48.8682" "-126.128_1" "48.2539" "-160.128" "40.6201"
## [1511] "-120.968" "-213.991" "191.817" "-171.862" "-79.4756"
## [1516] "28.1797" "45.9922" "-199.642" "-71.5586" "-101.034"
## [1521] "-47.5957" "-74.7393_1" "-91.916" "-57.5625" "-26.0371"
## [1526] "66.1377" "-91.6338" "-98.207" "-349.071" "-174.548"
## [1531] "-14.4443" "-139.063" "-169.741" "-202.822" "-41.1641"
## [1536] "-90.3613" "27.1191" "-201.126" "-8.29492_1" "-61.2383"
## [1541] "-64.0654" "-304.61" "-82.0908_1" "-19.7461" "3.43945"
## [1546] "-155.18" "-35.7207" "-118.848" "-210.174" "-332.248"
## [1551] "-192.997" "-108.951" "-103.721_1" "-79.4043" "-133.975"
## [1556] "-117.434" "-19.958_1" "63.0986" "-58.1279" "-22.3613"
## [1561] "-233.218" "-100.469" "-245.446" "-170.802" "116.537"
## [1566] "-280.294" "-154.544" "-163.733" "-197.238" "-249.899"
## [1571] "18.3545_1" "-281.708" "-169.317" "-70.2861" "-126.693"
## [1576] "-92.7646" "-116.373_1" "-249.404" "-28.1572" "-15.9287"
## [1581] "49.1025" "-168.54" "-82.7266" "-136.59" "45.7803"
## [1586] "144.67" "351.992" "165.664" "156.687" "82.1123"
## [1591] "72.3584" "125.726" "428.191" "362.171" "321.385"
## [1596] "578.611" "578.046" "599.251" "832.656" "827.072"
## [1601] "827.072_1"DTzred <- DTz[,-348:-352]Now lets plot again …. Does it looks better ?
p <- plot_ly(z = ~DTzred) %>% add_surface()
pElse repeat the previous step For this execute the following code. Be sure to run it on the previously cleaned object. In this case DTzred Be sure to check again the columns numbers sinsce these have changed
colnames(DTzred)
DTzred <- DTzred[,-348:-352]Now that you have the cleaned data object lets have a look at the 2d map. Be patient, this one is longer to plot.
p <- plot_ly(mtrx.melt, x = ~sample, y = ~ppm, z = ~int, type = "contour",
colors = 'YlOrRd',
autocontour = F,
contours = list(
start = 10000,
end = 1200000,
size = 5000
)
)
pIf you want to plot the map with ppm on the x-axis just reverse the axis order. Play with start value (to fix the noise) and size value to fix the contour space. Change color if you wish by changing the color field. For more info on 2d contour plot with plotly check https://plot.ly/r/contour-plots/
p <- plot_ly(mtrx.melt, x = ~ppm, y = ~sample, z = ~int, type = "contour",
autocontour = F,
colors = 'YlOrRd',
contours = list(
start = 10000,
end = 1200000,
size = 50000
)
) %>% layout(xaxis = list(autorange = "reversed"))
p